Hi everyone, when am doing this g_dist between the protein and water am getting the distance between water-water. why it is so?? and is there a way i can find distance in each time frame.
Thanks On Thu, Sep 8, 2011 at 5:55 PM, aiswarya pawar <aiswarya.pa...@gmail.com>wrote: > Hi users, > > To get the distance between water and protein i did - > > g_dist -f md.xtc -s md.tpr -o distance.xvg -dist 1 -b 1 -e 11 > > from this i should obtain an output file as distance.xvg which i dont get. > > and my output is printed on the terminal as- > > t: 1 136 SOL 2336 OW 0.772373 (nm) > t: 1 136 SOL 2337 HW1 0.706358 (nm) > t: 1 136 SOL 2338 HW2 0.807787 (nm) > t: 1 139 SOL 2345 OW 0.821094 (nm) > t: 1 139 SOL 2346 HW1 0.810919 (nm) > t: 1 139 SOL 2347 HW2 0.771526 (nm) > t: 1 7237 SOL 23640 HW1 0.997056 (nm) > t: 1 11793 SOL 37307 OW 0.868929 (nm) > t: 1 11793 SOL 37308 HW1 0.927205 (nm) > t: 1 11793 SOL 37309 HW2 0.776699 (nm) > t: 2 125 SOL 2303 OW 0.940527 (nm) > > In this > > t: 1 136 SOL 2336 OW 0.772373 (nm) > > does the 't' states the time frame, 136 SOL states the SOL molecule number > and 2336 OW the residue contact from protein and the 0.772373 nm the > distance between them. > > Thanks > >
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